HEAD is a pointer to a commit (usually master) so when you checkout your repository the commit which HEAD points at will be checked out. Usually you'd want it if when checking out you want a different branch or tag to be checked out.
You can take a look at what it's pointing out by issuing the following command:
And you'll probably see something like the following: origin/HEAD -> origin/master
You can delete HEAD if you don't need it (although it doesn't do any harm being there) by issuing the following command:
Note: on github there is already an checkbox you can check under Settings > Options.